Toll to add/remove dummy atoms from linearities or multi-hapto sites. More...

Collaboration diagram for denoptim.utils.DummyAtomHandler:

Public Member Functions
	DummyAtomHandler (String elm, Logger logger)
	Constructor defining a specific elemental symbol to consider the symbol of dummy atoms. More...

IAtomContainer	removeDummy (IAtomContainer mol)
	Removes all dummy atoms and the bonds connecting them to other atoms. More...

IAtomContainer	removeDummyInHapto (IAtomContainer mol) throws DENOPTIMException

Static Public Member Functions
static void	addDummiesOnLinearities (Fragment frag, double angLim)
	Append dummy atoms on otherwise linear arrangements of atoms. More...

static IAtom	getDummyInSafeDirection (IAtom atmA, Point3d pB, IAtomContainer mol, List< Point3d > placesToAvoid)
	Generates a dummy atom 0.1 nm from atom A in a place that is safe for a dummy atom. More...

Package Attributes
int	recNum = 1

Private Member Functions
Set< IAtom >	exploreConnectedToAtom (IAtom seed, List< IAtom > inList, IAtomContainer mol, List< Boolean > doneFlag)
	Explore connected systems in a list of atoms and returns all the atoms that can be reached starting from the seed atom by moving only along connections between atoms in the initial list. More...

List< Boolean >	getFlagsVector (int size)
	Generates a vector of boolean flags. More...

Static Private Member Functions
static int	getSDFAtomNumber (IAtomContainer mol, IAtom atm)

Private Attributes
String	elm = ""
	The elemental symbol that we consider to be the symbol of a dummy atom. More...

Logger	logger
	Program-specific logger. More...

Detailed Description

Toll to add/remove dummy atoms from linearities or multi-hapto sites.

Author: Marco Foscato; Vishwesh Venkatraman

Definition at line 53 of file DummyAtomHandler.java.

Constructor & Destructor Documentation

◆ DummyAtomHandler()

denoptim.utils.DummyAtomHandler.DummyAtomHandler	(	String	elm,
		Logger	logger
	)

Constructor defining a specific elemental symbol to consider the symbol of dummy atoms.

Parameters

elm	the elemental symbol that we consider to be the symbol of a dummy atom.
logger

Definition at line 78 of file DummyAtomHandler.java.

References denoptim.utils.DummyAtomHandler.elm, and denoptim.utils.DummyAtomHandler.logger.

Member Function Documentation

◆ addDummiesOnLinearities()

static void denoptim.utils.DummyAtomHandler.addDummiesOnLinearities	(	Fragment	frag,
		double	angLim
	)

static

Append dummy atoms on otherwise linear arrangements of atoms.

This to allow the use of internal coordinates when doing 3d-modeling. Dummy atoms are connected to the central atom of a linear (or close-to-linear) bend. Attachment points are also taken into account. Dummy atoms with no attachment point and only one connected neighbor are assumed to be linearity-breaking dummy atoms. Therefore, no additional dummy is added on central atoms that already have such neighbor.

Parameters

frag	the fragment to be modified.
angLim	the upper limit for an angle before we consider it flat, i.e., 180 DEG angle.

Definition at line 427 of file DummyAtomHandler.java.

Referenced by denoptim.gui.GUIVertexInspector.initialize(), denoptim.ga.EAUtils.makeGraphFromFragmentationOfMol(), denoptim.fragmenter.FragmenterTools.manageFragmentCollection(), and denoptim.graph.FragmentTest.testIsomorphicInLinear().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ exploreConnectedToAtom()

Set< IAtom > denoptim.utils.DummyAtomHandler.exploreConnectedToAtom	(	IAtom	seed,
		List< IAtom >	inList,
		IAtomContainer	mol,
		List< Boolean >	doneFlag
	)

private

Explore connected systems in a list of atoms and returns all the atoms that can be reached starting from the seed atom by moving only along connections between atoms in the initial list.

Parameters

seed	the atom from which to start
inList	list of atoms to be considered
mol	the molecular object containing all atoms in inList
doneFlag	vector of boolean flags

Returns: the group of atoms reachable via bonds between atoms in inList

Definition at line 358 of file DummyAtomHandler.java.

References denoptim.utils.DummyAtomHandler.exploreConnectedToAtom(), and denoptim.utils.DummyAtomHandler.recNum.

Referenced by denoptim.utils.DummyAtomHandler.exploreConnectedToAtom(), and denoptim.utils.DummyAtomHandler.removeDummyInHapto().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ getDummyInSafeDirection()

static IAtom denoptim.utils.DummyAtomHandler.getDummyInSafeDirection	(	IAtom	atmA,
		Point3d	pB,
		IAtomContainer	mol,
		List< Point3d >	placesToAvoid
	)

static

Generates a dummy atom 0.1 nm from atom A in a place that is safe for a dummy atom.

The be safe the position of the dummy has to respect 2 criteria:

be not too close to an existing atom connected to A,
be not too close to be opposite to an atom connected to A, which means, do not create linearities.

The method try to use 90 and 45 DEG with respect to vector departing from atom A in direction given by point B.

Parameters

atmA	first atom used to place the dummy
pB	point defining the direction of interest when placing the dummy atom.
mol	the molecular system
placesToAvoid	points from which the new dummy should stay away.

Returns: the dummy atom

Definition at line 514 of file DummyAtomHandler.java.

References denoptim.constants.DENOPTIMConstants.DUMMYATMSYMBOL, denoptim.utils.CartesianSpaceUtils.getDiffOfVector(), denoptim.utils.CartesianSpaceUtils.getNormalDirection(), denoptim.utils.MoleculeUtils.getPoint3d(), denoptim.utils.CartesianSpaceUtils.getSumOfVector(), denoptim.utils.CartesianSpaceUtils.getVectorFromTo(), denoptim.utils.CartesianSpaceUtils.rotatedVectorWAxisAngle(), and denoptim.utils.CartesianSpaceUtils.translateOrigin().

Referenced by denoptim.utils.DummyAtomHandler.addDummiesOnLinearities().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ getFlagsVector()

List< Boolean > denoptim.utils.DummyAtomHandler.getFlagsVector ( int size )

private

Generates a vector of boolean flags.

The size of the vector equals the number of atoms in the IAtomContainer. All flags are initialized to false.

Parameters


  
    size of vector of flags has to be generated.


Returns
a vector of flags.

Definition at line 395 of file DummyAtomHandler.java.

Referenced by denoptim.utils.DummyAtomHandler.removeDummyInHapto().

Here is the caller graph for this function:

◆ getSDFAtomNumber()

static int denoptim.utils.DummyAtomHandler.getSDFAtomNumber	(	IAtomContainer	mol,
		IAtom	atm
	)

staticprivate

Definition at line 407 of file DummyAtomHandler.java.

Referenced by denoptim.utils.DummyAtomHandler.removeDummy(), and denoptim.utils.DummyAtomHandler.removeDummyInHapto().

Here is the caller graph for this function:

◆ removeDummy()

IAtomContainer denoptim.utils.DummyAtomHandler.removeDummy ( IAtomContainer mol )

Removes all dummy atoms and the bonds connecting them to other atoms.

Definition at line 90 of file DummyAtomHandler.java.

References denoptim.constants.DENOPTIMConstants.DUMMYATMSYMBOL, denoptim.utils.DummyAtomHandler.elm, denoptim.utils.DummyAtomHandler.getSDFAtomNumber(), denoptim.utils.MoleculeUtils.getSymbolOrLabel(), denoptim.utils.DummyAtomHandler.logger, and denoptim.io.DenoptimIO.NL.

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure(), denoptim.fitness.FitnessProvider.getFitness(), and denoptim.utils.MoleculeUtils.getSMILESForMolecule().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ removeDummyInHapto()

IAtomContainer denoptim.utils.DummyAtomHandler.removeDummyInHapto ( IAtomContainer mol ) throws DENOPTIMException

Definition at line 144 of file DummyAtomHandler.java.

References denoptim.constants.DENOPTIMConstants.DUMMYATMSYMBOL, denoptim.utils.DummyAtomHandler.elm, denoptim.utils.DummyAtomHandler.exploreConnectedToAtom(), denoptim.utils.DummyAtomHandler.getFlagsVector(), denoptim.utils.DummyAtomHandler.getSDFAtomNumber(), denoptim.utils.MoleculeUtils.getSymbolOrLabel(), denoptim.utils.DummyAtomHandler.logger, denoptim.io.DenoptimIO.NL, and denoptim.io.DenoptimIO.writeSDFFile().

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure(), denoptim.utils.MoleculeUtils.generate2DCoordinates(), denoptim.fitness.FitnessProvider.getFitness(), denoptim.utils.MoleculeUtils.getInChIKeyForMolecule(), and denoptim.utils.MoleculeUtils.getSMILESForMolecule().

Here is the call graph for this function:

Here is the caller graph for this function:

Member Data Documentation

◆ elm

String denoptim.utils.DummyAtomHandler.elm = ""

private

The elemental symbol that we consider to be the symbol of a dummy atom.

Definition at line 58 of file DummyAtomHandler.java.

Referenced by denoptim.utils.DummyAtomHandler.DummyAtomHandler(), denoptim.utils.DummyAtomHandler.removeDummy(), and denoptim.utils.DummyAtomHandler.removeDummyInHapto().

◆ logger

Logger denoptim.utils.DummyAtomHandler.logger

private

Program-specific logger.

Definition at line 66 of file DummyAtomHandler.java.

Referenced by denoptim.utils.DummyAtomHandler.DummyAtomHandler(), denoptim.utils.DummyAtomHandler.removeDummy(), and denoptim.utils.DummyAtomHandler.removeDummyInHapto().

◆ recNum

int denoptim.utils.DummyAtomHandler.recNum = 1

package

Definition at line 61 of file DummyAtomHandler.java.

Referenced by denoptim.utils.DummyAtomHandler.exploreConnectedToAtom().

The documentation for this class was generated from the following file:

/github/workspace/src/main/java/denoptim/utils/DummyAtomHandler.java

Public Member Functions

Static Public Member Functions

Package Attributes

Private Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ DummyAtomHandler()

Member Function Documentation

◆ addDummiesOnLinearities()

◆ exploreConnectedToAtom()

◆ getDummyInSafeDirection()

◆ getFlagsVector()

◆ getSDFAtomNumber()

◆ removeDummy()

◆ removeDummyInHapto()

Member Data Documentation

◆ elm

◆ logger

◆ recNum